Setup

## **** __Utilized Cores__ **** = 2$subsetGenes
## [1] "protein_coding"
## 
## $subsetCells
## [1] 500
## 
## $resolution
## [1] 0.6
## 
## $resultsPath
## [1] "./Results"
## 
## $nCores
## [1] 2
## 
## $perplexity
## [1] 30
## [1] "monocle3 0.1.2"
## class: cell_data_set 
## dim: 14827 19144 
## metadata(1): cds_version
## assays(1): counts
## rownames(14827): A1BG A2M ... ZZEF1 ZZZ3
## rowData names(1): gene_short_name
## colnames(19144): GTCATTTTCCGCATCT ATAAGAGAGGAGTTGC ...
##   CAGTAACCCGCTCGCA ACACCGGTCCGGCCCA
## colData names(23): nGene nUMI ... cell_type cluster_ext_type
## reducedDimNames(2): PCA UMAP
## spikeNames(0):

Differential Gene Expression

Detect whether or not to limit DGE analysis to only the top N most variable genes.

## [1] "Testing all 14827 genes in DGE analysis."

Across Clusters

PD vs. Control

## [1] "Results file already exists. Importing..."
## Warning: Removed 1197 rows containing missing values (geom_point).

PD vs. GBA

## [1] "Results file already exists. Importing..."
## Warning in max(neg.log.pvals): no non-missing arguments to max; returning -
## Inf
## Warning in max(abs(dge_sig$estimate)): no non-missing arguments to max;
## returning -Inf
## Warning: Removed 6 rows containing missing values (geom_text_repel).
## Warning: Removed 1 rows containing missing values (geom_hline).

Canonical vs. Intermediate Monocytes

  • Compare all Canonical Monocytes (Cluster 1) to all Intermediate Monocytes (Cluster 2), regardless of disease status.
## [1] "Results file already exists. Importing..."
## Warning: Removed 2527 rows containing missing values (geom_point).

Within Clusters

Disease

  • Compare PD vs. Controls DGE within each cluster.
  • Cluster 1 = Canonical Monocytes, Cluster 2 = Intermediate Monocytes.

Cluster 1

[1] “Results file already exists. Importing…”

## Warning: Removed 1419 rows containing missing values (geom_point).

Cluster 2

[1] “Results file already exists. Importing…”

## Warning: Removed 1957 rows containing missing values (geom_point).

PD vs. GBA

Cluster 1

[1] “Results file already exists. Importing…”

## Warning: Removed 1775 rows containing missing values (geom_point).

Cluster 2

[1] “Results file already exists. Importing…”

## Warning: Removed 2359 rows containing missing values (geom_point).

Top Specific Markers

  • Find genes that characterize each cluster.
  • Specifically, only compare Clusters 1 and 2 to focuses on differences between these.
## Warning in instance$preRenderHook(instance): It seems your data is too
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## https://rstudio.github.io/DT/server.html